BN1424 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 3.4693e-07 2.7479e-04
Layer 6 8.6060e-06 7.1728e-03
Layer 5 3.5303e-05 2.5300e-03
Layer 4 1.0938e-04 4.1714e-02
Layer 3 6.9555e-04 6.4794e-02
WM 7.5140e-02 2.6034e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.2646 0.7006
DLGAP1 Layer 2 2.3711 0.6990
ATP6V1H Layer 2 3.0000 0.6909
BEX2 Layer 2 2.5059 0.6833
DNAJA4 Layer 2 2.3965 0.6818
ARF1 Layer 2 2.3125 0.6817
HSPA12A Layer 2 2.2930 0.6786
MFSD4A Layer 2 2.9082 0.6755
LONRF2 Layer 2 2.7070 0.6740
SLC39A10 Layer 2 2.3281 0.6738
SERINC3 Layer 2 2.3281 0.6737
AP2B1 Layer 2 2.3027 0.6729
HSPA5 Layer 2 2.4512 0.6724
IQSEC2 Layer 2 2.3438 0.6713
PAK1 Layer 2 2.6191 0.6705
SUMO2 Layer 2 2.3086 0.6688
WASF1 Layer 2 2.5117 0.6675
CREG2 Layer 2 2.7305 0.6668
CRMP1 Layer 2 2.3086 0.6666
TMEM130 Layer 2 2.4785 0.6659
MRTFB Layer 2 2.7129 0.6653
PRRT1 Layer 2 2.3555 0.6649
KCNAB2 Layer 2 2.4668 0.6648
MDH1 Layer 2 2.4121 0.6643
PAFAH1B1 Layer 2 2.3711 0.6637
KIAA1549L Layer 2 2.6777 0.6637
TMEM170B Layer 2 2.3809 0.6629
PNMA8A Layer 2 2.3027 0.6628
MAP2K1 Layer 2 2.4883 0.6618
CAMK2D Layer 2 2.4785 0.6616
PNMA1 Layer 2 2.4336 0.6615
BEX4 Layer 2 2.3926 0.6605
GRIA2 Layer 2 2.6367 0.6604
KLHL2 Layer 2 2.3496 0.6602
PDE1A Layer 2 2.2715 0.6597
PTPRN2 Layer 2 2.3027 0.6581
ATP9A Layer 2 2.3340 0.6578
SCAMP5 Layer 2 2.2266 0.6573
AP1S1 Layer 2 2.6602 0.6570
CLIP3 Layer 2 2.2324 0.6568
BAIAP2 Layer 2 2.6250 0.6567
OCIAD1 Layer 2 2.3926 0.6560
GABARAPL2 Layer 2 2.3750 0.6558
NSG2 Layer 2 2.9609 0.6556
PJA2 Layer 2 2.3281 0.6555
UNC5A Layer 2 2.2676 0.6554
AKAP11 Layer 2 2.3125 0.6553
CAPNS1 Layer 2 2.1250 0.6550
NELL2 Layer 6 2.3184 0.6544
BEX1 Layer 2 2.5723 0.6540

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1424
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1424_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1424/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1424/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1424/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1424/report/PD/BN1424_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1424/report/PD/BN1424_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:09:32
  • Number of Processes: 10
  • Spending Time: 0h 4m